GO-CAM ectopic meeting July 19th 2017
Zoom URL
https://stanford.zoom.us/j/679970729
Agenda
Discussion of inference on Wnt signaling LEGO model
http://noctua.berkeleybop.org/editor/graph/gomodel:5966411600000538
Missing/New inferences:
contributes_to inference:
Added to RO: part of'(?x, ?y) ^ enables(?y, ?z) ^ molecular_function(?z) -> 'contributes to'(?x, ?z) e.g. GP(X) part_of complex(Y) enables MF(Z) -> X contributes_to Z
Annotation to compound molecular function => annotation to its parts
enables(?x, ?y) ^ 'has part'(?y, ?z) ^ molecular_function(?y) -> enables(?x, ?z)
e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'
Inferences from molecular function regulators
https://github.com/geneontology/go-ontology/issues/13492)
e.g.:
X <— enabled by— protein binding —directly_positively_regulates --> protein kinase activity —enabled_by--> Y
=>
X enables ‘protein binding activity' has_input Y * X enables 'protein kinase activator activity’ has_input Y *
\* Comes from a new rule:
molecular_function(?x) ^ molecular_function(?y) ^ 'directly regulates'(?x, ?y) ^ enables(?z, ?y) -> 'has input'(?x, ?z)
e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z
Wrong inferences that need to be trimmed:
regulates o part_of->regulates
https://github.com/geneontology/go-ontology/issues/13926#issuecomment-316054054
Strategies for trimming down superfluous inference
- enables and other GP/Complex -> MF/BP relations never go in extensions. Inference of the ‘contributes to’ qualifier would make up for this.
- some very high level classes should be blacklisted from extensions (molecular_function, regulation of molecular function. We could perhaps existing no annotation subset flags for these.)
- If we have ‘X regulation’ then the GPAD has only GP involved_in 'regulation of X', not GP involved_in_regulation_of X.
This is hard to implement: simpler alternative would be to just drop this GP-GO term relation and rely on named regulation classes alone